... better reefs ... premiere dives sites ...
There aren't any "better reefs". Honestly. I'm not being some sort of booster here.
I love Maracaibo - it's possibly my favorite dive - but it's deep, a short dive, and often involves deco. Some of my favorite dives have been long, shallow explorations at Paradise. Some days a site I usually like is sort of blah for one reason or another, and other sites shine more than usual. It hasn't always been the first time, but sooner or later with every site I've come to understand why I would want to go there again.
What makes a "good" dive site: Coral formations? Tiny critters? Do swim-throughs bore you? Do you fail to understand what excites people about splendid toadfish? Do you care about photography? Do you love to fly along the reef hardly kicking?
You're not very likely to find that nudibranch on a dive at Barracuda because you're not going to have any time to inspect the sandy bottom. If you love dramatic coral formations you might get bored with a 90-minute dive at San Clemente seahorse-hunting.
My point is that you must be clear about what would constitute "better reefs" or "premier dive sites" TO YOU in order to ensure that you get to them.
The real reason most of us prefer the boutique operators, besides the lack of a "cattle-boat" approach with large groups of sometimes poorly-matched divers and more regimented dive plans, is their flexibility and responsiveness. They don't have a schedule that says "Tuesday is Palancar Ladrones and Paso del Cedral". The divemasters and captains know the changing conditions and can take into account what divers are looking for and recommend sites that are likely to be great for those purposes that day.
Hotel Cozumel is fine (I've never tried the food, and never would), but I wouldn't likely ever dive with a hotel's "in-house" dive shop since in my view the range of independent shops offer much more value.